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Release Notes

All notable changes to SeroVerse and the SeroVerse ecosystem are documented on this page. This project adheres to Semantic Versioning and the Keep a Changelog specification.

[Unreleased]

Added

  • Structure-of-Arrays & Graph Core (seroverse.core):
  • BatchedContainer and RaggedArrayContainer zero-copy memory protocols (seroverse.core.collections).
  • Intervals (seroverse.core.interval) and GenomeAssembly (seroverse.core.genome, seroverse.core.io.fasta).
  • 2-bit DNA/RNA (Alphabet.DNA) and MMSEQS12 reduced amino-acid alphabets with ragged translation across NCBI translation tables (seroverse.core.seq.alphabet).
  • RandstrobeIndex (\(O(1)\) strobemer seeding) and FracMinHashIndex k-mer indices (seroverse.core.seq.kmers).
  • Vectorized unbanded/banded Smith-Waterman-Gotoh local and semi-global alignment (PairwiseAligner in seroverse.core.seq.pairwise).
  • Hybrid sequence + motif-rescued protein clustering (Clusterer supporting greedy incremental and sparse Markov Clustering MCL modes in seroverse.core.seq.clustering).
  • Packed CSR directed multigraphs (Graph, Graphs), Consensus Pan-Graph compression (GraphBatch.as_pan_graph), Hungarian + L2-QP GraphAligner, branch-and-bound maximum_spanning_arborescence, RelationalMPNN, and Fruchterman-Reingold LayoutEngine (seroverse.core.graph).
  • Async Repository & Metadata Clients (seroverse.client):
  • Async token-bucket rate-limited HTTP client (Client) and msgspec cassette serialization (cassette_context, encode_msgpack, decode_msgpack, load_msgpack, save_msgpack in seroverse.client.base).
  • NCBIClient (seroverse.client.ncbi), ENAClient (seroverse.client.ena), BacDiveClient & StrainInfoClient (seroverse.client.dsmz), and PathogenwatchBaseClient (seroverse.client.pathogenwatch).
  • Unified Ecosystem Documentation:
  • Unified Zensical documentation hub for SeroVerse, SeroRef, KBank, SeroGen, and SeroEpi with organization-wide GitHub Discussions announcements and Giscus comments.

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